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- PDB-2hey: Crystal structure of murine OX40L bound to human OX40 -

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Basic information

Entry
Database: PDB / ID: 2hey
TitleCrystal structure of murine OX40L bound to human OX40
Components
  • Tumor necrosis factor ligand superfamily member 4
  • Tumor necrosis factor receptor superfamily member 4
KeywordsCYTOKINE / receptor-ligan complex / co-stimulator / TNFSF
Function / homology
Function and homology information


positive regulation of immune effector process / cellular response to nitrogen dioxide / memory T cell activation / T-helper 2 cell activation / response to nitrogen dioxide / positive regulation of CD4-positive, alpha-beta T cell costimulation / positive regulation of interleukin-4-dependent isotype switching to IgE isotypes / positive regulation of T cell costimulation / positive regulation of T-helper 2 cell activation / defense response to nematode ...positive regulation of immune effector process / cellular response to nitrogen dioxide / memory T cell activation / T-helper 2 cell activation / response to nitrogen dioxide / positive regulation of CD4-positive, alpha-beta T cell costimulation / positive regulation of interleukin-4-dependent isotype switching to IgE isotypes / positive regulation of T cell costimulation / positive regulation of T-helper 2 cell activation / defense response to nematode / positive regulation of CD4-positive, alpha-beta T cell differentiation / negative regulation of activation-induced cell death of T cells / CD4-positive, alpha-beta T cell costimulation / TNFs bind their physiological receptors / positive regulation of immunoglobulin mediated immune response / regulation of adaptive immune response / negative regulation of T-helper 1 cell differentiation / tumor necrosis factor receptor superfamily binding / tumor necrosis factor receptor activity / negative regulation of regulatory T cell differentiation / positive regulation of T-helper 2 cell differentiation / TNFs bind their physiological receptors / acute inflammatory response / positive regulation of alpha-beta T cell proliferation / positive regulation of B cell activation / positive regulation of type 2 immune response / positive regulation of interleukin-13 production / negative regulation of T cell apoptotic process / positive regulation of memory T cell differentiation / negative regulation of interleukin-17 production / tumor necrosis factor receptor binding / negative regulation of cytokine production / positive regulation of immunoglobulin production / positive regulation of memory T cell activation / positive regulation of interleukin-4 production / blood vessel development / positive regulation of activated T cell proliferation / positive regulation of interleukin-10 production / negative regulation of type II interferon production / positive regulation of T cell migration / T cell proliferation / positive regulation of chemokine production / positive regulation of T cell proliferation / positive regulation of B cell proliferation / positive regulation of interleukin-12 production / positive regulation of interleukin-2 production / cholesterol metabolic process / positive regulation of cytokine production / cytokine activity / negative regulation of extrinsic apoptotic signaling pathway / response to virus / negative regulation of DNA-binding transcription factor activity / positive regulation of T cell cytokine production / positive regulation of inflammatory response / cellular response to prostaglandin E stimulus / positive regulation of interleukin-6 production / positive regulation of type II interferon production / virus receptor activity / regulation of inflammatory response / cellular response to lipopolysaccharide / inflammatory response / immune response / external side of plasma membrane / innate immune response / negative regulation of DNA-templated transcription / cell surface / extracellular space / membrane / plasma membrane
Similarity search - Function
Tumor necrosis factor ligand superfamily member 4 / Tumour necrosis factor receptor 4 / Tumour necrosis factor receptor 4, N-terminal / Tumor Necrosis Factor Receptor, subunit A, domain 2 / Tumor Necrosis Factor Receptor, subunit A; domain 2 / Tumour necrosis factor, conserved site / Tumor necrosis factor (TNF) homology domain (THD) signature. / Tumour necrosis factor family. / Tumour necrosis factor domain / TNFR/NGFR family cysteine-rich region domain profile. ...Tumor necrosis factor ligand superfamily member 4 / Tumour necrosis factor receptor 4 / Tumour necrosis factor receptor 4, N-terminal / Tumor Necrosis Factor Receptor, subunit A, domain 2 / Tumor Necrosis Factor Receptor, subunit A; domain 2 / Tumour necrosis factor, conserved site / Tumor necrosis factor (TNF) homology domain (THD) signature. / Tumour necrosis factor family. / Tumour necrosis factor domain / TNFR/NGFR family cysteine-rich region domain profile. / TNFR/NGFR cysteine-rich region / TNFR/NGFR family cysteine-rich region signature. / Tumor necrosis factor (TNF) homology domain (THD) profile. / Tumor necrosis factor receptor / nerve growth factor receptor repeats. / TNFR/NGFR cysteine-rich region / Jelly Rolls - #40 / Tumour necrosis factor-like domain superfamily / Putative ephrin-receptor like / Ribbon / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Tumor necrosis factor ligand superfamily member 4 / Tumor necrosis factor receptor superfamily member 4
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHymowitz, S.G.
CitationJournal: Structure / Year: 2006
Title: The Crystal Structure of the Costimulatory OX40-OX40L Complex.
Authors: Compaan, D.M. / Hymowitz, S.G.
History
DepositionJun 22, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
F: Tumor necrosis factor ligand superfamily member 4
G: Tumor necrosis factor ligand superfamily member 4
R: Tumor necrosis factor receptor superfamily member 4
T: Tumor necrosis factor receptor superfamily member 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,8425
Polymers65,7464
Non-polymers961
Water3,171176
1
F: Tumor necrosis factor ligand superfamily member 4
R: Tumor necrosis factor receptor superfamily member 4
hetero molecules

F: Tumor necrosis factor ligand superfamily member 4
R: Tumor necrosis factor receptor superfamily member 4
hetero molecules

F: Tumor necrosis factor ligand superfamily member 4
R: Tumor necrosis factor receptor superfamily member 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,9089
Polymers98,6196
Non-polymers2883
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-y+2,x-y+1,z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
2
G: Tumor necrosis factor ligand superfamily member 4
T: Tumor necrosis factor receptor superfamily member 4

G: Tumor necrosis factor ligand superfamily member 4
T: Tumor necrosis factor receptor superfamily member 4

G: Tumor necrosis factor ligand superfamily member 4
T: Tumor necrosis factor receptor superfamily member 4


Theoretical massNumber of molelcules
Total (without water)98,6196
Polymers98,6196
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Unit cell
Length a, b, c (Å)104.729, 104.729, 478.161
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11F-242-

HOH

21F-243-

HOH

31G-218-

HOH

DetailsThe biologically relevant assembly is a hetero-hexomer containing a ligand trimer bound to three copies of the receptor ECD. The two ligand-receptor complexes in the assymmetric unit generate two crystallographically independent biological assemblies via crystallographic 3-folds

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Components

#1: Protein Tumor necrosis factor ligand superfamily member 4 / OX40 ligand / OX40L / CD252 antigen


Mass: 17064.396 Da / Num. of mol.: 2 / Fragment: extracellular domain (residues 51-198)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tnfsf4, Ox40l, Txgp1l / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Hi5 / References: UniProt: P43488
#2: Protein Tumor necrosis factor receptor superfamily member 4 / OX40L receptor / ACT35 antigen / TAX transcriptionally-activated glycoprotein 1 receptor / CD134 antigen


Mass: 15808.759 Da / Num. of mol.: 2 / Fragment: extracellular domain (residues 29-170)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNFRSF4, TXGP1L / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Hi5 / References: UniProt: P43489
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.84 Å3/Da / Density % sol: 67.93 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M NaCl, 1.4 M Ammonium Sulfate, 0.1 M Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 21, 2003 / Details: torroidal mirror
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 68124 / Num. obs: 68124 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Rsym value: 0.069 / Net I/σ(I): 12.2
Reflection shellResolution: 2→2.07 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 6549 / Rsym value: 0.272 / % possible all: 96.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: murine OX40L

Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.927 / SU B: 5.995 / SU ML: 0.088 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.145 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24713 6853 10.1 %RANDOM
Rwork0.22054 ---
all0.2232 67693 --
obs0.2232 60840 98.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.815 Å2
Baniso -1Baniso -2Baniso -3
1-1.1 Å20.55 Å20 Å2
2--1.1 Å20 Å2
3----1.65 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4175 0 5 176 4356
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0224259
X-RAY DIFFRACTIONr_bond_other_d0.0010.023663
X-RAY DIFFRACTIONr_angle_refined_deg1.0411.9585799
X-RAY DIFFRACTIONr_angle_other_deg0.69238587
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7865537
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.9424.01192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.37115668
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.821530
X-RAY DIFFRACTIONr_chiral_restr0.0670.2626
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024781
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02825
X-RAY DIFFRACTIONr_nbd_refined0.1890.2672
X-RAY DIFFRACTIONr_nbd_other0.1730.23395
X-RAY DIFFRACTIONr_nbtor_refined0.1670.21977
X-RAY DIFFRACTIONr_nbtor_other0.0780.22518
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1180.2168
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.110.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1730.289
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.120.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4692.53484
X-RAY DIFFRACTIONr_mcbond_other0.3982.51087
X-RAY DIFFRACTIONr_mcangle_it3.07354384
X-RAY DIFFRACTIONr_scbond_it2.3352.51787
X-RAY DIFFRACTIONr_scangle_it3.34651415
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.06 Å / Total num. of bins used: 25
RfactorNum. reflection% reflection
Rfree0.293 374 -
Rwork0.236 3505 -
obs--97.12 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.40950.49890.42892.05270.52441.65730.061-0.15070.22330.1403-0.0410.1536-0.2464-0.2021-0.0199-0.09880.02270.031-0.12960.002-0.061243.9142102.7918174.8679
21.6896-0.07860.15092.6344-0.48682.02970.0348-0.301-0.07650.44860.0609-0.38840.02530.3677-0.09570.00550.0168-0.08470.06-0.0274-0.063814.610258.4872216.4521
31.59220.4407-0.71410.602-0.88825.1978-0.02330.0770.1890.0376-0.06320.1629-0.1226-0.1850.0865-0.1381-0.0493-0.0193-0.0932-0.0313-0.059525.668687.7196169.9556
48.3007-0.4453-5.46944.6111.13696.64620.7103-0.82090.95840.1917-0.08050.0379-1.07160.5838-0.62980.1474-0.21010.1620.1342-0.17490.006525.321593.6141196.7325
55.4047-3.3609-7.19659.72945.428622.1208-0.0919-0.26570.40590.55160.45740.6014-1.27130.1665-0.36540.4924-0.10130.23580.2599-0.20320.160816.8496100.8594213.0094
61.5274-0.2123-2.3410.8567-0.09578.63390.1399-0.35210.1940.3353-0.0519-0.2094-0.73450.719-0.0880.1643-0.17030.00850.0992-0.06480.065316.278181.5721211.5454
73.204-1.848310.34454.6424-1.550338.855-0.35520.6662-0.76940.22390.7654-0.51210.7252.1475-0.41020.4902-0.184-0.2380.353-0.46360.027218.209678.1285240.9816
827.71150.061513.48178.62422.462432.01190.09810.2481-0.3615-0.13640.4003-0.08230.22061.9882-0.49830.43820.10320.02170.4983-0.33350.274626.465481.7957256.4784
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1FA57 - 19111 - 145
2X-RAY DIFFRACTION2GB57 - 19011 - 144
3X-RAY DIFFRACTION3RC29 - 1085 - 84
4X-RAY DIFFRACTION4RC109 - 14085 - 116
5X-RAY DIFFRACTION5RC141 - 166117 - 142
6X-RAY DIFFRACTION6TD29 - 1085 - 84
7X-RAY DIFFRACTION7TD109 - 14085 - 116
8X-RAY DIFFRACTION8TD141 - 166117 - 142

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